auto

default_project_conf.py

@@ -13,12 +13,12 @@
 
 
 CLUSTERS['cee'] = {
-'address':'aksenov@10.30.16.62',
+'address':'aksenov@10.30.16.62', # command for ssh
 'homepath':'/home/aksenov/',
 'schedule':'SLURM',
 'corenum':16,
 'pythonpath':'/usr/lib64/python2.7/site-packages/numpy',
-'vasp_com':'prun /opt/vasp/bin/vasp5.4.1MPI',
+'vasp_com':'prun /opt/vasp/bin/vasp5.4.1MPI', # path to vasp binary
 }
 
 CLUSTERS['skol'] = {

header.py

@@ -17,28 +17,33 @@
 """
 
 import os, subprocess, sys, shelve
-
-import matplotlib as mpl
+try:
+    import matplotlib as mpl
 
 
 
-"""Global matplotlib control"""
-# size = 22 #for one coloumn figures
-size = 16 #for DOS
-# size = 16 #for two coloumn figures
-mpl.rc('font',family='Serif')
-# mpl.rc('xtick', labelsize= size) 
-# mpl.rc('ytick', labelsize= size) 
-# mpl.rc('axes', labelsize = size) 
-# mpl.rc('legend', fontsize= size) 
-# mpl.rc('Axes.annotate', fontsize= size) #does not work
-mpl.rcParams.update({'font.size': size})
-mpl.rcParams.update({'mathtext.fontset': "stix"})
-# plt.rcParams['mathtext.fontset'] = "stix"
+    """Global matplotlib control"""
+    # size = 22 #for one coloumn figures
+    size = 16 #for DOS
+    # size = 16 #for two coloumn figures
+    mpl.rc('font',family='Serif')
+    # mpl.rc('xtick', labelsize= size) 
+    # mpl.rc('ytick', labelsize= size) 
+    # mpl.rc('axes', labelsize = size) 
+    # mpl.rc('legend', fontsize= size) 
+    # mpl.rc('Axes.annotate', fontsize= size) #does not work
+    mpl.rcParams.update({'font.size': size})
+    mpl.rcParams.update({'mathtext.fontset': "stix"})
+    # plt.rcParams['mathtext.fontset'] = "stix"
 
-#paths to libraries needed by siman
-# sys.path.append('/home/dim/Simulation_wrapper/ase') #
+    #paths to libraries needed by siman
+    # sys.path.append('/home/dim/Simulation_wrapper/ase') #
+    import matplotlib.pyplot as plt
 
+except:
+    mpl = None
+    plt = None
+    print('Warning! matplotlib is not installed! Some functions will not work!')
 
 history = []
 
@@ -65,7 +70,6 @@
     warnings = 'yY'
 
 
-import matplotlib.pyplot as plt
 
 
 calc_database = 'only_calc.gdbm3'

picture_functions.py

@@ -142,7 +142,7 @@ def process_fig_filename(image_name, fig_format):
     else:
         path2saved = str(image_name)+'.'+fig_format
 
-    path2saved_png = os.path.dirname(image_name)+'/png/'+os.path.basename(image_name)+'.png'
+    path2saved_png = os.path.dirname(image_name)+'./png/'+os.path.basename(image_name)+'.png'
     makedir(path2saved_png)
 
     return path2saved, path2saved_png

tutorials/Configure.ipynb

@@ -0,0 +1,97 @@
+{
+ "metadata": {
+  "name": "",
+  "signature": "sha256:c2b8f74c3fcf2d06349ca03e41fba8a4af62d3dc9bc251a21b97c9b0eeb48429"
+ },
+ "nbformat": 3,
+ "nbformat_minor": 0,
+ "worksheets": [
+  {
+   "cells": [
+    {
+     "cell_type": "heading",
+     "level": 1,
+     "metadata": {},
+     "source": [
+      "Configuration of siman"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Configuration is provided in \"siman/default_project_conf.py\" file. Open it."
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {},
+     "source": [
+      "1. Configuration of cluster"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Find the code below and provide your address, your homepath, your schedule system (from 'PBS', 'SLURM', SGE),\n",
+      "number of cores, path to python (optional), and vasp_command - path to vasp binary on cluster"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "CLUSTERS['cee'] = {\n",
+      "'address':'aksenov@10.30.16.62', # command for ssh\n",
+      "'homepath':'/home/aksenov/',\n",
+      "'schedule':'SLURM',\n",
+      "'corenum':16,\n",
+      "'pythonpath':'/usr/lib64/python2.7/site-packages/numpy',\n",
+      "'vasp_com':'prun /opt/vasp/bin/vasp5.4.1MPI',  # path to vasp binary\n",
+      "}"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Attention! You should set up **passwordless** access to cluster. See here http://www.linuxproblem.org/art_9.html\n",
+      "\n",
+      "If you use some other schedule system on your cluster, use different ssh port, please ask developer."
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {},
+     "source": [
+      "2. Path to potentials"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Change the following string, which is the path to folder with VASP potentials"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "PATH2POTENTIALS = '/home/aksenov/scientific_projects/PAW_PBE_VASP'"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    }
+   ],
+   "metadata": {}
+  }
+ ]
+}